The issue is that Authorization header is also used to authenticate yourself to DreamFactory... Dreamfactory checks the header when you send it to see if you are authorized, and it sees the Authentication header that you want passed through. In our case this was throwing an error then, because the pass through Auth Bearer header is not JWT format, and so DreamFactory throws an error instead of ignoring it.
One way is to use a different header field "AuthorizationPassThru" for your pass thru token, and in AuthCheck.php -- AFTER user is authorized to DreamFactory, rewrite the Authorization header to your AuthorizationPassThru value if present.